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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcatgtttttgaatcttctgatgttaatatcagtttgattagggtctagacttagagattccaatgaataactttgtgatgtgttattgtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC

Basic information

species Glycine max
transcript GLYMA16G04800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
tctcatgtttttgaatcttctgatgttaatatcagtttgattagggtctagacttagagattccaatgaataa-ctttgtgatgtgttattgtc---cctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC
||| |||||    ||  | | | | ||   ||  |     || || |   |         |||   | | ||| ||| || |  | ||||   |    |  ||||| ||||||||||||||  | |||||  | |||||||||||||| |||||||| || |||||||| ||||| || |  || ||  |  | ||||| ||| 
tctgatgtt----aagttgccgctcttctcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG

upper sequence: GLYMA16G04800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
tctcatgtttt-tgaatcttctgatgttaatatcagtttgattagggtctagacttagagattccaatgaataactt-tgtgatgtgtt--attgtc-cctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC
   | | ||   | || |   |  |   || |  ||  | | |    ||| || ||     ||  ||    ||| || |||  | || |  ||||||      |||| ||||||||||||||  | ||||| ||||||||||||||||| ||  | ||||| |||||||| ||||||||    || || ||  | ||||  ||| 
---cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcct--ttttaacttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA

upper sequence: GLYMA16G04800.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G04090.1 (Arabidopsis thaliana), 3'ss of exon 2
tctcatgtttttgaatc-ttctgatgttaatatcagtttga-ttagggtc-tagacttagagattc-caatgaataactttgtgatgtgttattgtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC
   ||| | ||   ||| |||  |   |  ||       || ||| | |  ||   | | ||||     || ||| | | | |    |||  ||| |  ||||||| ||||| |||||||||||  ||| ||  |||||||||||||||||  |||| || ||||||||  |  | ||||  |||||| |||  ||||| | ||
---catatattcacatcattccaacactcttaaacccgagaattatgattgtatcttcaaagatagatgattaatcaatatctctcttgtgtttg-caatgcagGCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATCTACGTCTACTGGATCAGTTCTTTCGTAGGAGCATTATCTGCTGCATTGC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|193632303|gb|FK581887.1|FK581887
EST:     CTATTGGTTTGGTATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: C-A-TGG-TTGG-ATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
EST: gi|57574578|gb|CX547553.1|CX547553
EST:     TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
EST: gi|193491877|gb|FK457801.1|FK457801
EST:     GGTACATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: GGT-CATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
EST: gi|207768259|gb|GD739943.1|GD739943
EST:     TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
EST: gi|193713309|gb|FK651900.1|FK651900
EST:     TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
EST: gi|193563519|gb|FK519966.1|FK519966
EST:     TATTGGTTTGGTATTCTGCCTACACTGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: -A-TGG-TTGG-A-TCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
EST: gi|19348017|gb|BM892549.1|BM892549
EST:     TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
EST: gi|58019771|gb|CX706513.1|CX706513
EST:     TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
EST: gi|208207664|gb|GE007585.1|GE007585
EST:     TGGTCATGGTTGGATCTGCCTACACGGGGCCAGCCATGAATCCTGCCAAC                         GCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC
genomic: TGGTCATGGTTGGATCTGCCTACACTGGGCCAGCCATGAATCCTGCCAACgtgagtgatt ... gtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctagacttagagattccaatgaataactttgtgatgtgttattgtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC
                      gaataac  putative branch site (score: 2)
                                           ttgtccct  putative PPT
                   aatgaataa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcatgtttttgaatcttctgatgttaatatcagtttgattagggtctagacttagagattccaatgaataactttgtgatgtgttattgtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- tcatgtt
- - - - - - - - - tctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg